The First Protein Structure

Any discussion of protein structure must necessarily begin with myoglobin, because it is where the science of protein structure began. After years of arduous work, John Kendrew and his coworkers determined the atomic structure of myoglobin, laying the foundation for an era of biological understanding. You can take a close look at this protein structure yourself, in PDB entry 1mbn. You will be amazed, just like the world was in 1960, at the beautiful intricacy of this protein.

Myoglobin and Muscles

Myoglobin is a small, bright red protein. It is very common in muscle cells and gives meat much of its red color. Its job is to store oxygen, for use when muscles are hard at work. To do this, it uses a special chemical tool to capture slippery oxygen molecules: a heme group. Heme is a disk-shaped molecule that has a hole in the center that is perfect for holding an iron ion. The iron then forms a strong interaction with the oxygen molecule. As you can see in the structure, the heme group is held tightly in a deep pocket on one side of the protein.

Visualizing Protein Structure

When the structure of myoglobin was solved, it posed a great challenge. The structure is so complex that new methods needed to be developed to display and understand it. John Kendrew used a huge wire model to build the structure based on the experimental electron density. Then, the artist Irving Geis was employed to create a picture of myoglobin for a prominent article in Scientific American. Computer graphics were still many years in the future, so he created this illustration entirely by hand, one atom at a time. You can learn more about the work of Irving Geis at the Geis Archive on PDB-101.

Whale myoglobin has five more positively-charged amino acids than pig myoglobin. Three of the five are seen in this view, shown with stars. Positively-charged amino acids are in blue and negatively-charged ones are in red.

Myoglobin and Whales

If you look at John Kendrew's PDB file, you'll notice that the myoglobin he used was taken from sperm whale muscles. Whales and dolphin have a great need for myoglobin, so that they can store extra oxygen for use in their deep undersea dives. Typically, they have about 30 times more than in animals that live on land. A recent study revealed that a few special modifications are needed to make this possible. Comparing whale myoglobin (PDB entry 1mbn) with pig myoglobin (PDB entry 1pmb), we find that there are several mutations that add extra positively-charged amino acids to the surface. Marine animals typically have these extra charges on the surface of their myoglobin to help repel neighboring molecules and prevent aggregation when myoglobin is at high concentrations.

Oxygen Bound to Myoglobin

A later structure of myoglobin, PDB entry 1mbo, shows that oxygen binds to the iron atom deep inside the protein. So how does it get in and out? The answer is that the structure in the PDB is only one snapshot of the protein, caught when it is in a tightly-closed form. In reality, myoglobin (and all other proteins) is constantly in motion, performing small flexing and breathing motions. So, temporary openings constantly appear and disappear, allowing oxygen in and out.

Exploring the Structure

Structural Features of Myoglobin (PDB entry 1mbn)

The atomic structure of myoglobin revealed many of the basic principles of protein structure and stability. For instance, the structure showed that when the protein chain folds into a globular structure, carbon-rich amino acids are sheltered inside and charged amino acids are most often found on the surface, occasionally forming salt bridges that pair two opposite charges (shown here with circles). To explore some of these principles, click on the image for an interactive JSmol.

Topics for Further Discussion

You can use the sequence comparison tool to align the sequences of different myoglobins, looking for mutations. For instance, here is the alignment of whale and pig myoglobin used to create the illustration in this column.

PDB entry 2jho includes myoglobin poisoned by cyanide. Take a look and you'll see that the cyanide blocks the binding site for oxygen.

The RCSB PDB Molecule of the Month by David S. Goodsell (The Scripps Research Institute and the RCSB PDB) presents short accounts on selected molecules from the Protein Data Bank. Each installment includes an introduction to the structure and function of the molecule, a discussion of the relevance of the molecule to human health and welfare, and suggestions for how visitors might view these structures and access further details. More

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PDB-101 helps teachers, students, and the general public explore the 3D world of proteins and nucleic acids. Learning about their diverse shapes and functions helps to understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease to biological energy.

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